Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Estimating true evolutionary distances between genomes
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
On the Practical Solution of the Reversal Median Problem
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Algorithm engineering for parallel computation
Experimental algorithmics
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
Reversal and transposition medians
Theoretical Computer Science
A linear time algorithm for the inversion median problem in circular bacterial genomes
Journal of Discrete Algorithms
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
A Fast and Exact Algorithm for the Median of Three Problem--A Graph Decomposition Approach
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Genomic distances under deletions and insertions
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
A fast and exact algorithm for the perfect reversal median problem
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Improving inversion median computation using commuting reversals and cycle information
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Baculovirus phylogeny based on genome rearrangements
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Reactive stochastic local search algorithms for the genomic median problem
EvoCOP'08 Proceedings of the 8th European conference on Evolutionary computation in combinatorial optimization
On exploring genome rearrangement phylogenetic patterns
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
The transposition median problem is NP-complete
Theoretical Computer Science
A practical algorithm for ancestral rearrangement reconstruction
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
GASTS: parsimony scoring under rearrangements
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Quartet-based phylogeny reconstruction from gene orders
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
The median problem for the reversal distance in circular bacterial genomes
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Conservation of combinatorial structures in evolution scenarios
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Phylogeny reconstruction from gene-order data has attracted much attention over the last few years. The two software packages used for that purpose, BPAnalysis and GRAPPA, both use so-called breakpoint medians in their computations. Some of our past results indicate that using inversion scores rather than breakpoint scores in evaluating trees leads to the selection of better trees. On that basis, we conjectured that phylogeny reconstructions could be improved by using inversion medians, which minimize evolutionary distance under an inversions-only model of genome rearrangement. Recent algorithmic developments have made it possible to compute inversion medians for problems of realistic size.Our experimental studies unequivocally show that inversion medians are strongly preferable to breakpoint medians in the context of phylogenetic reconstruction from gene-order data. Improvements are most pronounced in the reconstruction of ancestral genomes, but are also evident in the topological accuracy of the reconstruction as well as, surprisingly, in the overall running time. Improvements are strongest for small average distances along tree edges and for evolutionary scenarios with a preponderance of inversion events, but occur in all cases, including evolutionary scenarios with high proportions of transpositions.All of our tests were run using our GRAPPA package, available (under GPL) at www.cs.unm.edu/~moret/GRAPPA; the next release will include the inversion median software we used in this study. The software used includes RevMed, developed by the authors and available at www.cs.unm.edu/~acs, and A. Caprara's inversion median code, generously made available for testing.